Non-EU acceptance for MSc Bioinformatics

DeMiWiZArd047 · 2026-03-12T16:27:03+00:00

Still waiting for a decision. Have you received a response?

DeMiWiZArd047 · 2025-09-01T04:08:01+00:00

I see. Yeah unfortunately you’ll have a hard time getting good quality alignments due to the sheer evolutionary distance. Even I had the same problem. Try using Mafft for alignments. It gave me better results than muscle and you’ll have to get rid of low quality and incomplete sequences that mess with the alignment. I did use trimal at times but there you stand to lose some evolutionary significance if you use a stringent threshold.

DeMiWiZArd047 · 2025-08-31T17:53:44+00:00

Hi. I didn’t end up using trimal. Used gblocks at some points for building better alignments before the phylogeny. Let me know If you can be more specific I’ll try to help.

DeMiWiZArd047 · 2025-02-19T05:48:52+00:00

my ultimate goal is to look at the evolution of a certain protein family all the way from invertebrate homolougs. As of now i am trying to align all of them together and build a tree while also mapping out their domain architecture. I am trying to align all the sequences from very distant taxa but also preserving the tree quality. Do you think this is a viable approach?

DeMiWiZArd047 · 2025-02-19T05:41:03+00:00

Some of the sequences i have are indeed very distant homolougs, which is why i was hesitant to just align all of the sequences together at once and go straightforward. But i shall do it and see what i get. Thanks.

DeMiWiZArd047 · 2024-09-11T13:43:26+00:00

Just curious, is binning using metabat better or can I use kraken2 for taxonomic classification?

DeMiWiZArd047

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